The presently running GABI-FUTURE-Kat II grant from PTJ / BMBF (German Ministry of Education and Research) has been extended to 2011-12-31. We will submit soon an extension proposal to continue the service to the community for 30 more months until June 2014.

Newly confirmed GABI-Kat lines have been donated to NASC. Since the current number of lines donated to NASC is now (since the last update in March) presented here, this is the last such note in the "News and History" area of the website.

Since September 2004, SimpleSearch was based on the TIGRv5 sequence data and genome annotation data set. With the new database release GK release 24, the following changes have been implemented:
- pseudochromosome sequences from TAIRv9 and 10 are now the basis for the prediction of insertion sites;
- TAIRv10 annotation data are used to qualify the predicted insertions as genome hits, gene hits or CDSi hit;
- UTR information is used to qualify "good" insertions as "TS2pA hits" (transcription start to polyA addition);
- reannotation of all our FSTs has been performed (see news of 2011-02-14) and the data are now available from SimpleSearch.
The new release contains data from 71.238 lines with genome hits. There are 18.908 genes with hits, and there are 13.038 genes with CDSi hits (for CDSi hits, only protein-coding genes are counted because there is no protein-CDS in RNA genes). During the next days, the FAQ page and other descriptions on our website will be updated to fit the new release.
Although we tested carefully, it might be that some bugs escaped. Please report problems (see footer of this page for Email address).

The presently running GABI-FUTURE-Kat II grant from PTJ / BMBF (German Ministry of Education and Research) will terminate at 2011-06-30. We are now submitting two extension proposals to continue the service to the community for initially 6 more months until December 2011, and then for another two years. We still get between 50 and 70 insertion allele requests each month, and transfer of confirmed lines to NASC continues. One problem to be addressed is the reduction of the germination frequency of the now more than 10 years old seed stocks. Obviously, a line and the respective insertion(s) is lost when the T2 seeds that we have in stock do not germinate any more.
In addition, the re-annotation of all our FSTs (including new data, see News article of 2011-02-14) yielded predictions of new GK insertion alleles for about 5.500 additional TAIRv10 protein-coding genes (pseudogenes and TEs not counted). Among these are:
- 837 protein-coding genes with "good" knock-out alleles (insertion predicted to be located in the 5'-UTR or CDSi region) that had no predicted insertion allele in GK, SALK, SAIL or Wisc before (see the summary table for Ath insertion mutant alleles at SIGnAL), these 837 genes are now covered by new "GABI-Kat only" alleles;
- 1087 protein-coding genes with "good" knock-out alleles that so had only 1 insertion allele in SALK, SAIL or Wisc, these genes are now covered by a 2nd allele from GABI-Kat;
- about 600 protein-coding genes with a 2nd GK allele where the first allele is also from GK and no other insertion allele has been predicted in the SALK, SAIL or Wisc populations.
We hope that provision of these additional alleles will be attractive to reviewers, and to argue for a continuation of GABI-Kat.

The web page "Publications" has been updated in two ways. First, the page is now updated automatically from our LIMS database and is no longer only a html list which needed manual editing. Second, we have screened the recent literature and added about 70 new papers to our list. This list is VERY important for us because the output in terms of papers relying in GK insertion mutants is one of the main components to justify the grant that pays for our community service.
We would be happy to get a note from you users for each paper you publish that uses GABI-Kat insertion mutants! This should be independent from the source of the seed you got - this can be NASC, ABRC or GABI-Kat directly.

A total of 199 newly confirmed GABI-Kat lines have been donated to NASC in January and February 2011. These donation batches contain 1.322 and 1.389 individual T3 seed bags (199 T3-sets). In total, 8.646 T3-sets of which each represents a single GABI-Kat line have been donated so far. These lines cover 8.737 confirmed insertion alleles.

We have re-analysed all our FSTs with an optimised FST analysis pipeline that relies on the latest genome assembly (TAIRv9, identical to the sequence used in TAIRv10). In addition, new FSTs accumulated since the last SimpleSearch database release (GK release 23v2) in 2008. Together, these actions yielded about 20.000 new FSTs which have been submittet to EMBL/GenBank (Accession numbers FR799760 to FR819654).
The data are also available from the Expert download page which offers several datasets in flat file format. The release ID is GK release 24. At present, SimpleSearch still relies on the previous dataset 23v2. As soon as the upcoming new version of SimpleSearch has been finalized, the new FSTs as well as new insertion site predictions that are based on TAIRv10 annotation will become available.

During last week, the last seeds of newly confirmed lines have left the lab for 2010. Since the coming holidays may interfere with international delivery, the next seed will be put into the mail not before the second week of 2010.
We wish all our users a Merry Christmas and a Happy New Year, and GREAT phenotypes for the experiments in 2011!